Multiple sequence alignment - TraesCS5D01G535100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G535100 chr5D 100.000 4700 0 0 1 4700 549230964 549226265 0.000000e+00 8680
1 TraesCS5D01G535100 chr5D 92.176 3106 147 37 795 3846 549262503 549259440 0.000000e+00 4301
2 TraesCS5D01G535100 chr5D 81.056 1647 234 36 1280 2897 549548153 549546556 0.000000e+00 1242
3 TraesCS5D01G535100 chr5D 79.915 1643 249 39 1280 2893 549430068 549428478 0.000000e+00 1131
4 TraesCS5D01G535100 chr5D 82.407 216 32 6 478 689 429321643 429321430 2.890000e-42 183
5 TraesCS5D01G535100 chr5B 92.170 2286 114 18 707 2959 700857049 700854796 0.000000e+00 3169
6 TraesCS5D01G535100 chr5B 87.206 1532 133 39 3219 4700 700845514 700843996 0.000000e+00 1685
7 TraesCS5D01G535100 chr5B 80.510 1647 244 40 1280 2897 701051702 701050104 0.000000e+00 1192
8 TraesCS5D01G535100 chr5B 90.244 246 16 3 2956 3193 700845755 700845510 9.820000e-82 315
9 TraesCS5D01G535100 chr5B 88.148 135 14 2 4568 4700 655631548 655631414 4.870000e-35 159
10 TraesCS5D01G535100 chr4A 90.022 2315 136 29 795 3052 620705093 620702817 0.000000e+00 2907
11 TraesCS5D01G535100 chr4A 89.809 785 52 12 3047 3827 620657559 620656799 0.000000e+00 981
12 TraesCS5D01G535100 chr4A 86.245 538 63 8 3595 4127 620647381 620646850 1.470000e-159 573
13 TraesCS5D01G535100 chr4A 81.989 533 62 24 4196 4700 620646829 620646303 5.620000e-114 422
14 TraesCS5D01G535100 chr4A 91.873 283 16 1 2 277 620649922 620649640 5.700000e-104 388
15 TraesCS5D01G535100 chr4A 86.822 129 14 1 4575 4700 648945851 648945723 1.760000e-29 141
16 TraesCS5D01G535100 chr7D 85.287 870 113 11 1274 2130 162823654 162822787 0.000000e+00 883
17 TraesCS5D01G535100 chr7D 79.160 643 98 12 2224 2832 162822659 162822019 3.380000e-111 412
18 TraesCS5D01G535100 chr7D 78.526 312 55 7 2224 2525 162794178 162793869 1.330000e-45 195
19 TraesCS5D01G535100 chr7D 89.076 119 12 1 4583 4700 411597098 411597216 3.790000e-31 147
20 TraesCS5D01G535100 chr7A 84.890 867 120 9 1274 2130 163617765 163616900 0.000000e+00 865
21 TraesCS5D01G535100 chr2D 84.125 863 113 12 1280 2140 110843195 110842355 0.000000e+00 813
22 TraesCS5D01G535100 chr2D 91.379 116 7 1 4568 4680 483870523 483870638 6.300000e-34 156
23 TraesCS5D01G535100 chr2A 83.991 862 116 11 1280 2140 107182762 107181922 0.000000e+00 808
24 TraesCS5D01G535100 chr2A 79.621 211 35 8 479 685 472332511 472332717 1.360000e-30 145
25 TraesCS5D01G535100 chr3D 82.511 223 34 5 477 696 300618482 300618702 1.730000e-44 191
26 TraesCS5D01G535100 chr3D 80.180 222 36 7 482 699 444916228 444916445 4.870000e-35 159
27 TraesCS5D01G535100 chr3D 78.355 231 38 11 477 700 452655126 452654901 6.340000e-29 139
28 TraesCS5D01G535100 chr1A 81.221 213 33 6 477 685 29247396 29247187 1.050000e-36 165
29 TraesCS5D01G535100 chr1A 83.453 139 12 6 4566 4700 22244064 22244195 8.260000e-23 119
30 TraesCS5D01G535100 chr1B 79.630 216 36 6 477 685 180520025 180519811 1.050000e-31 148
31 TraesCS5D01G535100 chr3A 79.808 208 36 6 478 682 215200704 215200908 3.790000e-31 147
32 TraesCS5D01G535100 chr6A 78.166 229 43 7 477 702 438276201 438276425 6.340000e-29 139
33 TraesCS5D01G535100 chr3B 86.486 111 11 4 4563 4670 51980520 51980629 8.260000e-23 119
34 TraesCS5D01G535100 chr7B 83.065 124 15 5 190 309 457395271 457395150 1.790000e-19 108


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G535100 chr5D 549226265 549230964 4699 True 8680.0 8680 100.000000 1 4700 1 chr5D.!!$R2 4699
1 TraesCS5D01G535100 chr5D 549259440 549262503 3063 True 4301.0 4301 92.176000 795 3846 1 chr5D.!!$R3 3051
2 TraesCS5D01G535100 chr5D 549546556 549548153 1597 True 1242.0 1242 81.056000 1280 2897 1 chr5D.!!$R5 1617
3 TraesCS5D01G535100 chr5D 549428478 549430068 1590 True 1131.0 1131 79.915000 1280 2893 1 chr5D.!!$R4 1613
4 TraesCS5D01G535100 chr5B 700854796 700857049 2253 True 3169.0 3169 92.170000 707 2959 1 chr5B.!!$R2 2252
5 TraesCS5D01G535100 chr5B 701050104 701051702 1598 True 1192.0 1192 80.510000 1280 2897 1 chr5B.!!$R3 1617
6 TraesCS5D01G535100 chr5B 700843996 700845755 1759 True 1000.0 1685 88.725000 2956 4700 2 chr5B.!!$R4 1744
7 TraesCS5D01G535100 chr4A 620702817 620705093 2276 True 2907.0 2907 90.022000 795 3052 1 chr4A.!!$R2 2257
8 TraesCS5D01G535100 chr4A 620656799 620657559 760 True 981.0 981 89.809000 3047 3827 1 chr4A.!!$R1 780
9 TraesCS5D01G535100 chr4A 620646303 620649922 3619 True 461.0 573 86.702333 2 4700 3 chr4A.!!$R4 4698
10 TraesCS5D01G535100 chr7D 162822019 162823654 1635 True 647.5 883 82.223500 1274 2832 2 chr7D.!!$R2 1558
11 TraesCS5D01G535100 chr7A 163616900 163617765 865 True 865.0 865 84.890000 1274 2130 1 chr7A.!!$R1 856
12 TraesCS5D01G535100 chr2D 110842355 110843195 840 True 813.0 813 84.125000 1280 2140 1 chr2D.!!$R1 860
13 TraesCS5D01G535100 chr2A 107181922 107182762 840 True 808.0 808 83.991000 1280 2140 1 chr2A.!!$R1 860

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
884 2469 0.179000 CCTGCTTCCCGCTCTATGTT 59.821 55.0 0.00 0.00 40.11 2.71 F
2419 4096 0.252421 TGCAGGAGTCAGACATCCCT 60.252 55.0 2.66 3.44 36.14 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 4254 0.326618 ATCCCAGATGGTCGGGTTCT 60.327 55.0 0.0 0.0 43.57 3.01 R
4288 6027 0.108329 ACATAGGGAACGCCGAAGTG 60.108 55.0 0.0 0.0 33.83 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.226200 TCACATACACACTGCACATTGC 59.774 45.455 0.00 0.00 45.29 3.56
132 133 2.916089 GTGATGATCGATCGAGCTCATG 59.084 50.000 29.47 0.00 33.17 3.07
138 139 1.219522 CGATCGAGCTCATGCATGCA 61.220 55.000 25.04 25.04 42.74 3.96
145 146 1.266989 AGCTCATGCATGCATCAATCG 59.733 47.619 30.07 18.31 42.74 3.34
176 177 2.292267 ACAACAGCAACAGGTCAAGAG 58.708 47.619 0.00 0.00 0.00 2.85
180 181 0.183492 AGCAACAGGTCAAGAGCCAA 59.817 50.000 0.00 0.00 0.00 4.52
226 234 3.110358 CGCATTACCTGTTGCAATCATG 58.890 45.455 0.59 2.81 38.80 3.07
300 507 6.513180 TCGCTATAAGTAATTTGGACAGAGG 58.487 40.000 0.00 0.00 0.00 3.69
309 516 5.941555 AATTTGGACAGAGGGAGTAGTAG 57.058 43.478 0.00 0.00 0.00 2.57
310 517 3.383698 TTGGACAGAGGGAGTAGTAGG 57.616 52.381 0.00 0.00 0.00 3.18
315 522 4.104420 GGACAGAGGGAGTAGTAGGTATCA 59.896 50.000 0.00 0.00 0.00 2.15
316 523 5.051409 ACAGAGGGAGTAGTAGGTATCAC 57.949 47.826 0.00 0.00 0.00 3.06
317 524 4.477581 ACAGAGGGAGTAGTAGGTATCACA 59.522 45.833 0.00 0.00 0.00 3.58
318 525 4.822896 CAGAGGGAGTAGTAGGTATCACAC 59.177 50.000 0.00 0.00 0.00 3.82
319 526 4.477581 AGAGGGAGTAGTAGGTATCACACA 59.522 45.833 0.00 0.00 0.00 3.72
320 527 5.134679 AGAGGGAGTAGTAGGTATCACACAT 59.865 44.000 0.00 0.00 0.00 3.21
321 528 6.332103 AGAGGGAGTAGTAGGTATCACACATA 59.668 42.308 0.00 0.00 0.00 2.29
322 529 6.305411 AGGGAGTAGTAGGTATCACACATAC 58.695 44.000 0.00 0.00 43.26 2.39
323 530 5.180868 GGGAGTAGTAGGTATCACACATACG 59.819 48.000 0.00 0.00 46.58 3.06
331 538 2.604046 ATCACACATACGGAGGAAGC 57.396 50.000 0.00 0.00 0.00 3.86
345 552 5.164954 CGGAGGAAGCTAATGAGTATAAGC 58.835 45.833 0.00 0.00 0.00 3.09
346 553 5.047660 CGGAGGAAGCTAATGAGTATAAGCT 60.048 44.000 0.00 0.00 0.00 3.74
347 554 6.151312 CGGAGGAAGCTAATGAGTATAAGCTA 59.849 42.308 0.00 0.00 31.89 3.32
348 555 7.147983 CGGAGGAAGCTAATGAGTATAAGCTAT 60.148 40.741 0.00 0.00 31.89 2.97
349 556 9.191479 GGAGGAAGCTAATGAGTATAAGCTATA 57.809 37.037 0.00 0.00 31.89 1.31
374 581 6.804770 AGCTTGTCGGAGTATATACACTAG 57.195 41.667 15.18 10.73 0.00 2.57
377 584 6.652481 GCTTGTCGGAGTATATACACTAGGTA 59.348 42.308 15.18 0.00 36.16 3.08
378 585 7.336427 GCTTGTCGGAGTATATACACTAGGTAT 59.664 40.741 15.18 2.13 44.76 2.73
379 586 9.881649 CTTGTCGGAGTATATACACTAGGTATA 57.118 37.037 15.18 11.27 46.22 1.47
380 587 9.881649 TTGTCGGAGTATATACACTAGGTATAG 57.118 37.037 15.18 3.73 45.57 1.31
381 588 9.259832 TGTCGGAGTATATACACTAGGTATAGA 57.740 37.037 15.18 8.46 45.57 1.98
445 652 9.410556 GTACTAGAAAAACGTCTTACATTACCA 57.589 33.333 0.00 0.00 0.00 3.25
446 653 8.302965 ACTAGAAAAACGTCTTACATTACCAC 57.697 34.615 0.00 0.00 0.00 4.16
447 654 6.219302 AGAAAAACGTCTTACATTACCACG 57.781 37.500 0.00 0.00 36.54 4.94
448 655 4.394099 AAAACGTCTTACATTACCACGC 57.606 40.909 0.00 0.00 33.73 5.34
449 656 2.728690 ACGTCTTACATTACCACGCA 57.271 45.000 0.00 0.00 33.73 5.24
451 658 3.391965 ACGTCTTACATTACCACGCAAA 58.608 40.909 0.00 0.00 33.73 3.68
479 686 9.490379 AAGTCTTACATTAAGTTACAGAAGGTG 57.510 33.333 0.00 0.00 37.10 4.00
481 688 6.588756 TCTTACATTAAGTTACAGAAGGTGCG 59.411 38.462 0.00 0.00 37.10 5.34
483 690 3.396260 TTAAGTTACAGAAGGTGCGCT 57.604 42.857 9.73 0.00 0.00 5.92
484 691 4.524316 TTAAGTTACAGAAGGTGCGCTA 57.476 40.909 9.73 0.00 0.00 4.26
486 693 1.893801 AGTTACAGAAGGTGCGCTAGT 59.106 47.619 9.73 0.00 0.00 2.57
487 694 2.094649 AGTTACAGAAGGTGCGCTAGTC 60.095 50.000 9.73 0.46 0.00 2.59
491 698 1.683917 CAGAAGGTGCGCTAGTCCTAT 59.316 52.381 9.73 1.70 0.00 2.57
492 699 1.683917 AGAAGGTGCGCTAGTCCTATG 59.316 52.381 9.73 0.00 0.00 2.23
493 700 1.681793 GAAGGTGCGCTAGTCCTATGA 59.318 52.381 9.73 0.00 0.00 2.15
494 701 1.323412 AGGTGCGCTAGTCCTATGAG 58.677 55.000 9.73 0.00 0.00 2.90
495 702 0.315568 GGTGCGCTAGTCCTATGAGG 59.684 60.000 9.73 0.00 36.46 3.86
496 703 0.319125 GTGCGCTAGTCCTATGAGGC 60.319 60.000 9.73 0.00 34.61 4.70
498 705 1.182385 GCGCTAGTCCTATGAGGCCT 61.182 60.000 3.86 3.86 34.61 5.19
499 706 1.333177 CGCTAGTCCTATGAGGCCTT 58.667 55.000 6.77 0.00 34.61 4.35
500 707 2.515854 CGCTAGTCCTATGAGGCCTTA 58.484 52.381 6.77 1.66 34.61 2.69
503 710 2.478872 AGTCCTATGAGGCCTTAGCA 57.521 50.000 6.77 0.00 42.56 3.49
505 712 1.040646 TCCTATGAGGCCTTAGCACG 58.959 55.000 6.77 0.00 42.56 5.34
506 713 1.040646 CCTATGAGGCCTTAGCACGA 58.959 55.000 6.77 0.00 42.56 4.35
507 714 1.620819 CCTATGAGGCCTTAGCACGAT 59.379 52.381 6.77 0.00 42.56 3.73
510 717 2.596904 TGAGGCCTTAGCACGATAAC 57.403 50.000 6.77 0.00 42.56 1.89
511 718 1.828595 TGAGGCCTTAGCACGATAACA 59.171 47.619 6.77 0.00 42.56 2.41
514 721 3.467803 AGGCCTTAGCACGATAACATTC 58.532 45.455 0.00 0.00 42.56 2.67
515 722 2.548480 GGCCTTAGCACGATAACATTCC 59.452 50.000 0.00 0.00 42.56 3.01
516 723 3.202906 GCCTTAGCACGATAACATTCCA 58.797 45.455 0.00 0.00 39.53 3.53
517 724 3.625764 GCCTTAGCACGATAACATTCCAA 59.374 43.478 0.00 0.00 39.53 3.53
518 725 4.275936 GCCTTAGCACGATAACATTCCAAT 59.724 41.667 0.00 0.00 39.53 3.16
519 726 5.751680 CCTTAGCACGATAACATTCCAATG 58.248 41.667 0.00 0.00 42.10 2.82
531 738 5.705609 ACATTCCAATGTTCTACCACAAC 57.294 39.130 0.00 0.00 46.95 3.32
532 739 5.136828 ACATTCCAATGTTCTACCACAACA 58.863 37.500 0.00 0.00 46.95 3.33
533 740 5.596361 ACATTCCAATGTTCTACCACAACAA 59.404 36.000 0.00 0.00 46.95 2.83
534 741 5.766150 TTCCAATGTTCTACCACAACAAG 57.234 39.130 0.00 0.00 37.30 3.16
536 743 5.630121 TCCAATGTTCTACCACAACAAGAT 58.370 37.500 0.00 0.00 37.30 2.40
537 744 6.068010 TCCAATGTTCTACCACAACAAGATT 58.932 36.000 0.00 0.00 37.30 2.40
538 745 6.549364 TCCAATGTTCTACCACAACAAGATTT 59.451 34.615 0.00 0.00 37.30 2.17
541 748 6.371809 TGTTCTACCACAACAAGATTTGTC 57.628 37.500 0.00 0.00 44.59 3.18
542 749 5.298276 TGTTCTACCACAACAAGATTTGTCC 59.702 40.000 0.00 0.00 44.59 4.02
543 750 4.062293 TCTACCACAACAAGATTTGTCCG 58.938 43.478 0.00 0.00 44.59 4.79
545 752 1.335872 CCACAACAAGATTTGTCCGGC 60.336 52.381 0.00 0.00 44.59 6.13
546 753 1.608590 CACAACAAGATTTGTCCGGCT 59.391 47.619 0.00 0.00 44.59 5.52
547 754 2.034558 CACAACAAGATTTGTCCGGCTT 59.965 45.455 0.00 0.00 44.59 4.35
548 755 2.034558 ACAACAAGATTTGTCCGGCTTG 59.965 45.455 13.65 13.65 44.59 4.01
549 756 2.270352 ACAAGATTTGTCCGGCTTGA 57.730 45.000 19.93 0.00 40.56 3.02
550 757 2.795329 ACAAGATTTGTCCGGCTTGAT 58.205 42.857 19.93 2.61 40.56 2.57
551 758 2.489329 ACAAGATTTGTCCGGCTTGATG 59.511 45.455 19.93 4.91 40.56 3.07
561 768 2.899339 GCTTGATGAGCGAGGGGC 60.899 66.667 0.00 0.00 42.46 5.80
594 801 2.776913 GCCTTCGGCTCGCTCTAGT 61.777 63.158 0.00 0.00 46.69 2.57
597 804 1.999071 CTTCGGCTCGCTCTAGTGCT 61.999 60.000 14.40 0.00 0.00 4.40
598 805 1.595993 TTCGGCTCGCTCTAGTGCTT 61.596 55.000 14.40 0.00 0.00 3.91
600 807 1.216710 GGCTCGCTCTAGTGCTTGT 59.783 57.895 14.40 0.00 0.00 3.16
601 808 0.456221 GGCTCGCTCTAGTGCTTGTA 59.544 55.000 14.40 0.00 0.00 2.41
602 809 1.135083 GGCTCGCTCTAGTGCTTGTAA 60.135 52.381 14.40 0.00 0.00 2.41
603 810 2.482142 GGCTCGCTCTAGTGCTTGTAAT 60.482 50.000 14.40 0.00 0.00 1.89
604 811 2.792116 GCTCGCTCTAGTGCTTGTAATC 59.208 50.000 14.40 0.00 0.00 1.75
606 813 4.615949 CTCGCTCTAGTGCTTGTAATCAT 58.384 43.478 14.40 0.00 0.00 2.45
607 814 4.611943 TCGCTCTAGTGCTTGTAATCATC 58.388 43.478 14.40 0.00 0.00 2.92
608 815 3.423536 CGCTCTAGTGCTTGTAATCATCG 59.576 47.826 14.40 0.00 0.00 3.84
609 816 3.183373 GCTCTAGTGCTTGTAATCATCGC 59.817 47.826 9.52 0.00 0.00 4.58
610 817 4.615949 CTCTAGTGCTTGTAATCATCGCT 58.384 43.478 0.00 0.00 0.00 4.93
611 818 5.763088 CTCTAGTGCTTGTAATCATCGCTA 58.237 41.667 0.00 0.00 0.00 4.26
612 819 5.763088 TCTAGTGCTTGTAATCATCGCTAG 58.237 41.667 0.00 0.00 38.04 3.42
613 820 3.722147 AGTGCTTGTAATCATCGCTAGG 58.278 45.455 0.00 0.00 0.00 3.02
614 821 3.133003 AGTGCTTGTAATCATCGCTAGGT 59.867 43.478 0.00 0.00 0.00 3.08
616 823 3.871006 TGCTTGTAATCATCGCTAGGTTG 59.129 43.478 0.00 0.00 0.00 3.77
617 824 3.871594 GCTTGTAATCATCGCTAGGTTGT 59.128 43.478 0.00 0.00 0.00 3.32
619 826 5.339008 TTGTAATCATCGCTAGGTTGTCT 57.661 39.130 0.00 0.00 0.00 3.41
620 827 4.682787 TGTAATCATCGCTAGGTTGTCTG 58.317 43.478 0.00 0.00 0.00 3.51
623 830 1.204704 TCATCGCTAGGTTGTCTGTGG 59.795 52.381 0.00 0.00 0.00 4.17
624 831 1.204704 CATCGCTAGGTTGTCTGTGGA 59.795 52.381 0.00 0.00 0.00 4.02
626 1348 1.476891 TCGCTAGGTTGTCTGTGGATC 59.523 52.381 0.00 0.00 0.00 3.36
634 1356 4.532126 AGGTTGTCTGTGGATCTGAATGTA 59.468 41.667 0.00 0.00 0.00 2.29
636 1358 5.882557 GGTTGTCTGTGGATCTGAATGTATT 59.117 40.000 0.00 0.00 0.00 1.89
637 1359 6.375455 GGTTGTCTGTGGATCTGAATGTATTT 59.625 38.462 0.00 0.00 0.00 1.40
638 1360 7.094205 GGTTGTCTGTGGATCTGAATGTATTTT 60.094 37.037 0.00 0.00 0.00 1.82
639 1361 8.299570 GTTGTCTGTGGATCTGAATGTATTTTT 58.700 33.333 0.00 0.00 0.00 1.94
664 1386 7.486802 TTACTTTAGTGTTCTTTGTGCTACC 57.513 36.000 0.00 0.00 0.00 3.18
666 1388 6.120220 ACTTTAGTGTTCTTTGTGCTACCTT 58.880 36.000 0.00 0.00 0.00 3.50
667 1389 6.038271 ACTTTAGTGTTCTTTGTGCTACCTTG 59.962 38.462 0.00 0.00 0.00 3.61
668 1390 4.150897 AGTGTTCTTTGTGCTACCTTGA 57.849 40.909 0.00 0.00 0.00 3.02
669 1391 4.718961 AGTGTTCTTTGTGCTACCTTGAT 58.281 39.130 0.00 0.00 0.00 2.57
670 1392 5.865085 AGTGTTCTTTGTGCTACCTTGATA 58.135 37.500 0.00 0.00 0.00 2.15
671 1393 5.934625 AGTGTTCTTTGTGCTACCTTGATAG 59.065 40.000 0.00 0.00 0.00 2.08
673 1395 6.204882 GTGTTCTTTGTGCTACCTTGATAGTT 59.795 38.462 0.00 0.00 0.00 2.24
674 1396 7.386848 GTGTTCTTTGTGCTACCTTGATAGTTA 59.613 37.037 0.00 0.00 0.00 2.24
675 1397 7.934665 TGTTCTTTGTGCTACCTTGATAGTTAA 59.065 33.333 0.00 0.00 0.00 2.01
677 1399 8.492673 TCTTTGTGCTACCTTGATAGTTAATG 57.507 34.615 0.00 0.00 0.00 1.90
678 1400 8.318412 TCTTTGTGCTACCTTGATAGTTAATGA 58.682 33.333 0.00 0.00 0.00 2.57
679 1401 8.856153 TTTGTGCTACCTTGATAGTTAATGAA 57.144 30.769 0.00 0.00 0.00 2.57
680 1402 9.461312 TTTGTGCTACCTTGATAGTTAATGAAT 57.539 29.630 0.00 0.00 0.00 2.57
682 1404 9.764363 TGTGCTACCTTGATAGTTAATGAATAG 57.236 33.333 0.00 0.00 0.00 1.73
683 1405 9.982651 GTGCTACCTTGATAGTTAATGAATAGA 57.017 33.333 0.00 0.00 0.00 1.98
702 1424 9.988815 TGAATAGATAGAAAGCTTTCCTCATAC 57.011 33.333 30.83 19.59 37.92 2.39
703 1425 9.988815 GAATAGATAGAAAGCTTTCCTCATACA 57.011 33.333 30.83 16.10 37.92 2.29
705 1427 7.667575 AGATAGAAAGCTTTCCTCATACAGA 57.332 36.000 30.83 9.43 37.92 3.41
788 1733 5.984926 CAGTACAAGGTTTGATTTGCATGTT 59.015 36.000 0.00 0.00 0.00 2.71
789 1734 6.144402 CAGTACAAGGTTTGATTTGCATGTTC 59.856 38.462 0.00 0.00 0.00 3.18
849 2431 1.370657 GCGTCTTCGATCCTAGCCG 60.371 63.158 0.00 0.00 39.71 5.52
860 2442 4.845580 CTAGCCGCCCTGCACCTG 62.846 72.222 0.00 0.00 0.00 4.00
882 2467 1.596477 GCCTGCTTCCCGCTCTATG 60.596 63.158 0.00 0.00 40.11 2.23
883 2468 1.826024 CCTGCTTCCCGCTCTATGT 59.174 57.895 0.00 0.00 40.11 2.29
884 2469 0.179000 CCTGCTTCCCGCTCTATGTT 59.821 55.000 0.00 0.00 40.11 2.71
885 2470 1.407437 CCTGCTTCCCGCTCTATGTTT 60.407 52.381 0.00 0.00 40.11 2.83
886 2471 2.158957 CCTGCTTCCCGCTCTATGTTTA 60.159 50.000 0.00 0.00 40.11 2.01
887 2472 3.531538 CTGCTTCCCGCTCTATGTTTAA 58.468 45.455 0.00 0.00 40.11 1.52
888 2473 3.267483 TGCTTCCCGCTCTATGTTTAAC 58.733 45.455 0.00 0.00 40.11 2.01
889 2474 3.267483 GCTTCCCGCTCTATGTTTAACA 58.733 45.455 0.00 0.00 35.14 2.41
1055 2667 1.979469 CCATCGAGATAGCGCGTTTAG 59.021 52.381 8.43 0.00 38.51 1.85
1186 2804 0.256752 TAGCATGGCAATGGAGCAGT 59.743 50.000 2.54 0.00 34.09 4.40
1269 2887 2.034687 AAGGACAGCAAGCCGCAT 59.965 55.556 0.00 0.00 46.13 4.73
1947 3577 0.824109 TCGACGGCCATGAGAAGATT 59.176 50.000 2.24 0.00 0.00 2.40
1968 3598 1.898574 CAAGGAGGCCAACGCAACT 60.899 57.895 5.01 0.00 36.38 3.16
1973 3603 1.009829 GAGGCCAACGCAACTATGAG 58.990 55.000 5.01 0.00 36.38 2.90
1986 3616 2.906182 CTATGAGCCGGCTGCACGAA 62.906 60.000 38.41 17.80 44.83 3.85
2021 3651 2.228480 GGTGGGGGCAGTGGAAGTA 61.228 63.158 0.00 0.00 0.00 2.24
2055 3685 2.093973 GGAGCTTGATGACTTCCTCGAA 60.094 50.000 0.00 0.00 0.00 3.71
2211 3881 7.768120 TCAAACATTTACAAGGTGCAAAAGAAT 59.232 29.630 0.00 0.00 0.00 2.40
2338 4015 2.815211 GCAGAGATGGCGAACGCA 60.815 61.111 20.16 7.53 44.11 5.24
2419 4096 0.252421 TGCAGGAGTCAGACATCCCT 60.252 55.000 2.66 3.44 36.14 4.20
2430 4107 1.554160 AGACATCCCTCAACTCAGCTG 59.446 52.381 7.63 7.63 0.00 4.24
2525 4207 1.238625 CCAACGTTGCCGGTTACCAT 61.239 55.000 22.93 0.00 38.78 3.55
2572 4254 4.680237 CCGCACTGGACTCGGCAA 62.680 66.667 0.00 0.00 42.00 4.52
2600 4282 1.475169 CCATCTGGGATGAGCCGCTA 61.475 60.000 8.85 0.00 40.01 4.26
2671 4362 0.600557 ACAGAGAACGAGCTGAGGTG 59.399 55.000 0.00 0.00 36.07 4.00
2850 4556 1.156736 GATGTGTGCTAAGCCACGTT 58.843 50.000 0.00 0.00 38.55 3.99
2875 4581 4.814294 GCACCTCTACCACGCCGG 62.814 72.222 0.00 0.00 42.50 6.13
2930 4637 5.068234 TGGAAATAATATAGCTCGGTCGG 57.932 43.478 0.00 0.00 0.00 4.79
2932 4639 5.100943 GGAAATAATATAGCTCGGTCGGTC 58.899 45.833 0.00 0.00 0.00 4.79
2999 4706 2.358898 AGGTTTCTGTGCACACATGTTC 59.641 45.455 17.42 4.41 41.01 3.18
3005 4712 0.670162 GTGCACACATGTTCTTGGCT 59.330 50.000 13.17 0.00 0.00 4.75
3110 4821 8.251750 TCTTAGTGGTCATTTCGAAATAGTTG 57.748 34.615 22.33 12.42 0.00 3.16
3194 4909 6.488006 GCATCATTCTAACAAGTCCACCATAT 59.512 38.462 0.00 0.00 0.00 1.78
3200 4915 9.975218 ATTCTAACAAGTCCACCATATAAAACT 57.025 29.630 0.00 0.00 0.00 2.66
3405 5124 5.921408 CGAATCCCCACGATAAAAACAAAAA 59.079 36.000 0.00 0.00 0.00 1.94
3425 5144 5.914085 AAAGAGAGAAAACAGACGACATG 57.086 39.130 0.00 0.00 0.00 3.21
3438 5157 6.106673 ACAGACGACATGTATAAAAGGAAGG 58.893 40.000 0.00 0.00 0.00 3.46
3534 5254 2.385013 TATGAAGCTGCTGCGAAGAA 57.615 45.000 1.35 0.00 45.42 2.52
3619 5339 1.355971 TGCTAAAAGCTTAGACCGCG 58.644 50.000 0.00 0.00 42.97 6.46
3693 5415 3.123621 CAGACTGTTCAAATGCTACCGTC 59.876 47.826 0.00 0.00 0.00 4.79
3717 5440 7.122204 GTCCTACCAATAAAGTGTTAAGGCAAT 59.878 37.037 0.00 0.00 0.00 3.56
3744 5467 8.715191 AAACTGAATTTTTGTAGCAACATTGA 57.285 26.923 0.00 0.00 34.97 2.57
3745 5468 7.698836 ACTGAATTTTTGTAGCAACATTGAC 57.301 32.000 0.00 0.00 34.97 3.18
3757 5480 8.140628 TGTAGCAACATTGACACAAAATATGTT 58.859 29.630 0.00 0.00 41.46 2.71
3804 5532 2.598589 CAAATTTGATCTGCACACCGG 58.401 47.619 13.08 0.00 0.00 5.28
3827 5555 5.123979 GGGAGATGAACAATACAAAGTCACC 59.876 44.000 0.00 0.00 0.00 4.02
3829 5557 5.880901 AGATGAACAATACAAAGTCACCCT 58.119 37.500 0.00 0.00 0.00 4.34
3830 5558 5.940470 AGATGAACAATACAAAGTCACCCTC 59.060 40.000 0.00 0.00 0.00 4.30
3887 5617 5.990668 AGGTATCTTTGGATGAGGTTGTAC 58.009 41.667 0.00 0.00 33.71 2.90
3889 5619 5.817816 GGTATCTTTGGATGAGGTTGTACTG 59.182 44.000 0.00 0.00 33.71 2.74
3918 5648 7.172019 GGTAGGATTTGTCGTTCTTGTTTCTTA 59.828 37.037 0.00 0.00 0.00 2.10
3925 5655 8.609478 TTGTCGTTCTTGTTTCTTAATTTGTC 57.391 30.769 0.00 0.00 0.00 3.18
4041 5774 2.263895 AGTACCACCAGGATAGGCAA 57.736 50.000 0.00 0.00 38.69 4.52
4058 5791 3.708563 GCAACAACTCAGCCAACTTAA 57.291 42.857 0.00 0.00 0.00 1.85
4074 5807 5.534654 CCAACTTAATCTCACCCTGAAACAA 59.465 40.000 0.00 0.00 0.00 2.83
4118 5851 2.822701 GCGGATGGACGGTTTCCC 60.823 66.667 0.00 0.00 45.17 3.97
4142 5875 1.459450 CAACGGAGGGTAATGGGTTG 58.541 55.000 0.00 0.00 0.00 3.77
4170 5903 3.686227 TCCAATTTGGACATATGGGCT 57.314 42.857 14.24 0.00 42.67 5.19
4173 5906 5.523588 TCCAATTTGGACATATGGGCTAAA 58.476 37.500 14.24 9.33 42.67 1.85
4190 5923 3.808174 GCTAAATACCTCTAAACCGCCTG 59.192 47.826 0.00 0.00 0.00 4.85
4217 5950 0.107654 AGACTCAAATAGCCGGCCAC 60.108 55.000 26.15 4.09 0.00 5.01
4227 5960 2.510906 CCGGCCACTCCTATTGGG 59.489 66.667 2.24 0.00 34.35 4.12
4228 5961 2.510906 CGGCCACTCCTATTGGGG 59.489 66.667 2.24 0.00 40.50 4.96
4233 5971 2.006415 CACTCCTATTGGGGGCCCA 61.006 63.158 26.86 4.56 45.63 5.36
4288 6027 3.074369 CCAAATTGGACCGGCCCC 61.074 66.667 6.04 5.29 40.96 5.80
4309 6062 1.006832 CTTCGGCGTTCCCTATGTTG 58.993 55.000 6.85 0.00 0.00 3.33
4316 6069 3.254903 GGCGTTCCCTATGTTGTTTTCTT 59.745 43.478 0.00 0.00 0.00 2.52
4319 6072 6.440436 GCGTTCCCTATGTTGTTTTCTTTTA 58.560 36.000 0.00 0.00 0.00 1.52
4322 6075 9.124807 CGTTCCCTATGTTGTTTTCTTTTATTC 57.875 33.333 0.00 0.00 0.00 1.75
4362 6129 7.327975 AGTTTTCTCTTTCCGGATTTGTTTTT 58.672 30.769 4.15 0.00 0.00 1.94
4392 6163 5.182001 TGATTTTCTCTTCTTACAGGCTTGC 59.818 40.000 0.00 0.00 0.00 4.01
4529 6304 5.406649 TCAAAACACGCTGAACATTTTTCT 58.593 33.333 0.00 0.00 0.00 2.52
4534 6309 9.691362 AAAACACGCTGAACATTTTTCTAATAT 57.309 25.926 0.00 0.00 0.00 1.28
4600 6380 7.684317 TTTTAGGGGAAAAGGAGTTTCATTT 57.316 32.000 1.63 0.00 46.47 2.32
4622 6402 9.613428 CATTTCATATTTAGGGAGTTACAGTCA 57.387 33.333 0.00 0.00 0.00 3.41
4633 6413 4.762251 GGAGTTACAGTCAAGAGGCAAAAT 59.238 41.667 0.00 0.00 0.00 1.82
4636 6416 7.121315 GGAGTTACAGTCAAGAGGCAAAATATT 59.879 37.037 0.00 0.00 0.00 1.28
4648 6428 8.174733 AGAGGCAAAATATTCTCAATACATGG 57.825 34.615 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.239681 AGTTTTAAAAAGCAAACACTCTCAAC 57.760 30.769 1.31 0.00 0.00 3.18
13 14 7.305993 GCAGTGTGTATGTGAGTTTTAAAAAGC 60.306 37.037 1.31 0.00 0.00 3.51
90 91 0.034574 TCACCACCACCATACATGCC 60.035 55.000 0.00 0.00 0.00 4.40
132 133 0.109873 GCTAGCCGATTGATGCATGC 60.110 55.000 11.82 11.82 0.00 4.06
138 139 1.303309 GTTGCAGCTAGCCGATTGAT 58.697 50.000 12.13 0.00 44.83 2.57
176 177 2.093606 GGGAGTACTGGTTAGTCTTGGC 60.094 54.545 0.00 0.00 38.36 4.52
180 181 2.356947 CGGAGGGAGTACTGGTTAGTCT 60.357 54.545 0.00 0.00 38.36 3.24
277 484 5.696724 CCCTCTGTCCAAATTACTTATAGCG 59.303 44.000 0.00 0.00 0.00 4.26
295 502 4.822896 GTGTGATACCTACTACTCCCTCTG 59.177 50.000 0.00 0.00 0.00 3.35
296 503 4.477581 TGTGTGATACCTACTACTCCCTCT 59.522 45.833 0.00 0.00 0.00 3.69
300 507 5.180868 CCGTATGTGTGATACCTACTACTCC 59.819 48.000 0.00 0.00 30.80 3.85
309 516 3.799232 GCTTCCTCCGTATGTGTGATACC 60.799 52.174 0.00 0.00 0.00 2.73
310 517 3.068307 AGCTTCCTCCGTATGTGTGATAC 59.932 47.826 0.00 0.00 0.00 2.24
315 522 3.704566 TCATTAGCTTCCTCCGTATGTGT 59.295 43.478 0.00 0.00 0.00 3.72
316 523 4.202161 ACTCATTAGCTTCCTCCGTATGTG 60.202 45.833 0.00 0.00 0.00 3.21
317 524 3.961408 ACTCATTAGCTTCCTCCGTATGT 59.039 43.478 0.00 0.00 0.00 2.29
318 525 4.592485 ACTCATTAGCTTCCTCCGTATG 57.408 45.455 0.00 0.00 0.00 2.39
319 526 7.363094 GCTTATACTCATTAGCTTCCTCCGTAT 60.363 40.741 0.00 0.00 34.64 3.06
320 527 6.072064 GCTTATACTCATTAGCTTCCTCCGTA 60.072 42.308 0.00 0.00 34.64 4.02
321 528 5.279056 GCTTATACTCATTAGCTTCCTCCGT 60.279 44.000 0.00 0.00 34.64 4.69
322 529 5.047660 AGCTTATACTCATTAGCTTCCTCCG 60.048 44.000 0.00 0.00 42.95 4.63
323 530 6.353404 AGCTTATACTCATTAGCTTCCTCC 57.647 41.667 0.00 0.00 42.95 4.30
348 555 9.597170 CTAGTGTATATACTCCGACAAGCTATA 57.403 37.037 13.89 0.00 32.19 1.31
349 556 7.553402 CCTAGTGTATATACTCCGACAAGCTAT 59.447 40.741 13.89 0.00 32.19 2.97
350 557 6.877855 CCTAGTGTATATACTCCGACAAGCTA 59.122 42.308 13.89 2.96 32.19 3.32
351 558 5.706369 CCTAGTGTATATACTCCGACAAGCT 59.294 44.000 13.89 0.00 32.19 3.74
352 559 5.472820 ACCTAGTGTATATACTCCGACAAGC 59.527 44.000 13.89 0.00 32.19 4.01
354 561 9.881649 CTATACCTAGTGTATATACTCCGACAA 57.118 37.037 13.89 0.00 40.70 3.18
355 562 9.259832 TCTATACCTAGTGTATATACTCCGACA 57.740 37.037 13.89 0.00 40.70 4.35
418 625 9.631452 GGTAATGTAAGACGTTTTTCTAGTACT 57.369 33.333 0.00 0.00 0.00 2.73
419 626 9.410556 TGGTAATGTAAGACGTTTTTCTAGTAC 57.589 33.333 0.00 0.00 0.00 2.73
420 627 9.410556 GTGGTAATGTAAGACGTTTTTCTAGTA 57.589 33.333 0.00 0.00 0.00 1.82
421 628 7.115378 CGTGGTAATGTAAGACGTTTTTCTAGT 59.885 37.037 0.00 0.00 0.00 2.57
423 630 6.128849 GCGTGGTAATGTAAGACGTTTTTCTA 60.129 38.462 0.00 0.00 32.66 2.10
426 633 4.272991 TGCGTGGTAATGTAAGACGTTTTT 59.727 37.500 0.00 0.00 32.66 1.94
428 635 3.391965 TGCGTGGTAATGTAAGACGTTT 58.608 40.909 0.00 0.00 32.66 3.60
430 637 2.728690 TGCGTGGTAATGTAAGACGT 57.271 45.000 0.00 0.00 32.66 4.34
431 638 4.392619 TTTTGCGTGGTAATGTAAGACG 57.607 40.909 0.00 0.00 0.00 4.18
455 662 7.411588 CGCACCTTCTGTAACTTAATGTAAGAC 60.412 40.741 2.11 0.00 39.09 3.01
456 663 6.588756 CGCACCTTCTGTAACTTAATGTAAGA 59.411 38.462 2.11 0.00 39.09 2.10
457 664 6.672357 GCGCACCTTCTGTAACTTAATGTAAG 60.672 42.308 0.30 0.00 41.51 2.34
458 665 5.121142 GCGCACCTTCTGTAACTTAATGTAA 59.879 40.000 0.30 0.00 0.00 2.41
459 666 4.628333 GCGCACCTTCTGTAACTTAATGTA 59.372 41.667 0.30 0.00 0.00 2.29
461 668 3.684788 AGCGCACCTTCTGTAACTTAATG 59.315 43.478 11.47 0.00 0.00 1.90
462 669 3.939066 AGCGCACCTTCTGTAACTTAAT 58.061 40.909 11.47 0.00 0.00 1.40
464 671 3.508793 ACTAGCGCACCTTCTGTAACTTA 59.491 43.478 11.47 0.00 0.00 2.24
465 672 2.299297 ACTAGCGCACCTTCTGTAACTT 59.701 45.455 11.47 0.00 0.00 2.66
467 674 2.260481 GACTAGCGCACCTTCTGTAAC 58.740 52.381 11.47 0.00 0.00 2.50
468 675 1.203994 GGACTAGCGCACCTTCTGTAA 59.796 52.381 11.47 0.00 0.00 2.41
469 676 0.815734 GGACTAGCGCACCTTCTGTA 59.184 55.000 11.47 0.00 0.00 2.74
470 677 0.900647 AGGACTAGCGCACCTTCTGT 60.901 55.000 11.47 0.00 0.00 3.41
473 680 1.681793 TCATAGGACTAGCGCACCTTC 59.318 52.381 11.47 0.00 35.52 3.46
474 681 1.683917 CTCATAGGACTAGCGCACCTT 59.316 52.381 11.47 0.00 35.52 3.50
475 682 1.323412 CTCATAGGACTAGCGCACCT 58.677 55.000 11.47 14.90 37.76 4.00
476 683 0.315568 CCTCATAGGACTAGCGCACC 59.684 60.000 11.47 7.54 37.67 5.01
477 684 0.319125 GCCTCATAGGACTAGCGCAC 60.319 60.000 11.47 0.00 37.67 5.34
478 685 1.464376 GGCCTCATAGGACTAGCGCA 61.464 60.000 11.47 0.00 41.45 6.09
479 686 1.290639 GGCCTCATAGGACTAGCGC 59.709 63.158 0.00 0.00 41.45 5.92
486 693 1.040646 CGTGCTAAGGCCTCATAGGA 58.959 55.000 5.23 3.07 37.67 2.94
487 694 1.040646 TCGTGCTAAGGCCTCATAGG 58.959 55.000 5.23 0.00 38.80 2.57
491 698 1.828595 TGTTATCGTGCTAAGGCCTCA 59.171 47.619 5.23 0.00 37.74 3.86
492 699 2.596904 TGTTATCGTGCTAAGGCCTC 57.403 50.000 5.23 0.00 37.74 4.70
493 700 3.467803 GAATGTTATCGTGCTAAGGCCT 58.532 45.455 0.00 0.00 37.74 5.19
494 701 2.548480 GGAATGTTATCGTGCTAAGGCC 59.452 50.000 0.00 0.00 37.74 5.19
495 702 3.202906 TGGAATGTTATCGTGCTAAGGC 58.797 45.455 0.00 0.00 39.26 4.35
496 703 5.296780 ACATTGGAATGTTATCGTGCTAAGG 59.703 40.000 0.00 0.00 46.95 2.69
510 717 5.703978 TGTTGTGGTAGAACATTGGAATG 57.296 39.130 0.00 0.00 42.10 2.67
511 718 6.068010 TCTTGTTGTGGTAGAACATTGGAAT 58.932 36.000 0.00 0.00 33.41 3.01
514 721 5.964958 ATCTTGTTGTGGTAGAACATTGG 57.035 39.130 0.00 0.00 33.41 3.16
515 722 7.202526 ACAAATCTTGTTGTGGTAGAACATTG 58.797 34.615 0.00 0.00 42.22 2.82
516 723 7.346751 ACAAATCTTGTTGTGGTAGAACATT 57.653 32.000 0.00 0.00 42.22 2.71
517 724 6.016276 GGACAAATCTTGTTGTGGTAGAACAT 60.016 38.462 0.00 0.00 45.52 2.71
518 725 5.298276 GGACAAATCTTGTTGTGGTAGAACA 59.702 40.000 0.00 0.00 45.52 3.18
519 726 5.560183 CGGACAAATCTTGTTGTGGTAGAAC 60.560 44.000 0.00 0.00 45.52 3.01
522 729 3.188460 CCGGACAAATCTTGTTGTGGTAG 59.812 47.826 0.00 0.00 45.52 3.18
523 730 3.142951 CCGGACAAATCTTGTTGTGGTA 58.857 45.455 0.00 0.00 45.52 3.25
524 731 1.953686 CCGGACAAATCTTGTTGTGGT 59.046 47.619 0.00 0.00 45.52 4.16
526 733 1.608590 AGCCGGACAAATCTTGTTGTG 59.391 47.619 5.05 0.00 45.52 3.33
527 734 1.981256 AGCCGGACAAATCTTGTTGT 58.019 45.000 5.05 0.00 45.52 3.32
528 735 2.293122 TCAAGCCGGACAAATCTTGTTG 59.707 45.455 5.05 0.00 45.52 3.33
529 736 2.582052 TCAAGCCGGACAAATCTTGTT 58.418 42.857 5.05 0.00 45.52 2.83
531 738 2.749076 TCATCAAGCCGGACAAATCTTG 59.251 45.455 5.05 8.40 37.76 3.02
532 739 3.012518 CTCATCAAGCCGGACAAATCTT 58.987 45.455 5.05 0.00 0.00 2.40
533 740 2.636830 CTCATCAAGCCGGACAAATCT 58.363 47.619 5.05 0.00 0.00 2.40
534 741 1.064654 GCTCATCAAGCCGGACAAATC 59.935 52.381 5.05 0.00 45.92 2.17
536 743 2.555123 GCTCATCAAGCCGGACAAA 58.445 52.632 5.05 0.00 45.92 2.83
537 744 4.301505 GCTCATCAAGCCGGACAA 57.698 55.556 5.05 0.00 45.92 3.18
545 752 2.587194 CGCCCCTCGCTCATCAAG 60.587 66.667 0.00 0.00 34.21 3.02
546 753 4.161295 CCGCCCCTCGCTCATCAA 62.161 66.667 0.00 0.00 36.73 2.57
548 755 4.899239 CACCGCCCCTCGCTCATC 62.899 72.222 0.00 0.00 36.73 2.92
578 785 1.587613 GCACTAGAGCGAGCCGAAG 60.588 63.158 0.00 0.00 0.00 3.79
579 786 1.595993 AAGCACTAGAGCGAGCCGAA 61.596 55.000 6.51 0.00 40.15 4.30
580 787 2.046864 AAGCACTAGAGCGAGCCGA 61.047 57.895 6.51 0.00 40.15 5.54
581 788 1.875813 CAAGCACTAGAGCGAGCCG 60.876 63.158 6.51 0.00 40.15 5.52
582 789 0.456221 TACAAGCACTAGAGCGAGCC 59.544 55.000 6.51 0.00 40.15 4.70
583 790 2.279582 TTACAAGCACTAGAGCGAGC 57.720 50.000 6.51 0.00 40.15 5.03
584 791 4.033990 TGATTACAAGCACTAGAGCGAG 57.966 45.455 6.51 6.00 40.15 5.03
585 792 4.611943 GATGATTACAAGCACTAGAGCGA 58.388 43.478 6.51 0.00 40.15 4.93
586 793 3.423536 CGATGATTACAAGCACTAGAGCG 59.576 47.826 6.51 0.00 40.15 5.03
587 794 3.183373 GCGATGATTACAAGCACTAGAGC 59.817 47.826 3.68 3.68 35.16 4.09
588 795 4.615949 AGCGATGATTACAAGCACTAGAG 58.384 43.478 0.00 0.00 36.63 2.43
590 797 4.920340 CCTAGCGATGATTACAAGCACTAG 59.080 45.833 0.00 0.00 36.63 2.57
591 798 4.341235 ACCTAGCGATGATTACAAGCACTA 59.659 41.667 0.00 0.00 36.63 2.74
592 799 3.133003 ACCTAGCGATGATTACAAGCACT 59.867 43.478 0.00 0.00 36.63 4.40
594 801 3.819564 ACCTAGCGATGATTACAAGCA 57.180 42.857 0.00 0.00 36.63 3.91
597 804 5.109210 CAGACAACCTAGCGATGATTACAA 58.891 41.667 0.00 0.00 0.00 2.41
598 805 4.159693 ACAGACAACCTAGCGATGATTACA 59.840 41.667 0.00 0.00 0.00 2.41
600 807 4.441495 CCACAGACAACCTAGCGATGATTA 60.441 45.833 0.00 0.00 0.00 1.75
601 808 3.525537 CACAGACAACCTAGCGATGATT 58.474 45.455 0.00 0.00 0.00 2.57
602 809 2.159043 CCACAGACAACCTAGCGATGAT 60.159 50.000 0.00 0.00 0.00 2.45
603 810 1.204704 CCACAGACAACCTAGCGATGA 59.795 52.381 0.00 0.00 0.00 2.92
604 811 1.204704 TCCACAGACAACCTAGCGATG 59.795 52.381 0.00 0.00 0.00 3.84
606 813 1.476891 GATCCACAGACAACCTAGCGA 59.523 52.381 0.00 0.00 0.00 4.93
607 814 1.478510 AGATCCACAGACAACCTAGCG 59.521 52.381 0.00 0.00 0.00 4.26
608 815 2.497675 TCAGATCCACAGACAACCTAGC 59.502 50.000 0.00 0.00 0.00 3.42
609 816 4.808414 TTCAGATCCACAGACAACCTAG 57.192 45.455 0.00 0.00 0.00 3.02
610 817 4.532126 ACATTCAGATCCACAGACAACCTA 59.468 41.667 0.00 0.00 0.00 3.08
611 818 3.328931 ACATTCAGATCCACAGACAACCT 59.671 43.478 0.00 0.00 0.00 3.50
612 819 3.679389 ACATTCAGATCCACAGACAACC 58.321 45.455 0.00 0.00 0.00 3.77
613 820 6.992063 AATACATTCAGATCCACAGACAAC 57.008 37.500 0.00 0.00 0.00 3.32
614 821 8.408043 AAAAATACATTCAGATCCACAGACAA 57.592 30.769 0.00 0.00 0.00 3.18
637 1359 9.777575 GTAGCACAAAGAACACTAAAGTAAAAA 57.222 29.630 0.00 0.00 0.00 1.94
638 1360 8.400186 GGTAGCACAAAGAACACTAAAGTAAAA 58.600 33.333 0.00 0.00 0.00 1.52
639 1361 7.771826 AGGTAGCACAAAGAACACTAAAGTAAA 59.228 33.333 0.00 0.00 0.00 2.01
641 1363 6.823497 AGGTAGCACAAAGAACACTAAAGTA 58.177 36.000 0.00 0.00 0.00 2.24
642 1364 5.681639 AGGTAGCACAAAGAACACTAAAGT 58.318 37.500 0.00 0.00 0.00 2.66
643 1365 6.260050 TCAAGGTAGCACAAAGAACACTAAAG 59.740 38.462 0.00 0.00 0.00 1.85
647 1369 4.150897 TCAAGGTAGCACAAAGAACACT 57.849 40.909 0.00 0.00 0.00 3.55
654 1376 8.856153 TTCATTAACTATCAAGGTAGCACAAA 57.144 30.769 0.00 0.00 0.00 2.83
656 1378 9.764363 CTATTCATTAACTATCAAGGTAGCACA 57.236 33.333 0.00 0.00 0.00 4.57
657 1379 9.982651 TCTATTCATTAACTATCAAGGTAGCAC 57.017 33.333 0.00 0.00 0.00 4.40
677 1399 9.988815 TGTATGAGGAAAGCTTTCTATCTATTC 57.011 33.333 32.28 21.70 37.35 1.75
678 1400 9.995003 CTGTATGAGGAAAGCTTTCTATCTATT 57.005 33.333 32.28 21.01 37.35 1.73
679 1401 9.373450 TCTGTATGAGGAAAGCTTTCTATCTAT 57.627 33.333 32.28 24.48 37.35 1.98
680 1402 8.768501 TCTGTATGAGGAAAGCTTTCTATCTA 57.231 34.615 32.28 21.13 37.35 1.98
681 1403 7.667575 TCTGTATGAGGAAAGCTTTCTATCT 57.332 36.000 32.28 23.15 37.35 1.98
682 1404 7.945033 CTCTGTATGAGGAAAGCTTTCTATC 57.055 40.000 32.28 28.38 39.08 2.08
703 1425 3.371380 CCCTACGTACTTACAGACCCTCT 60.371 52.174 0.00 0.00 0.00 3.69
705 1427 2.578021 TCCCTACGTACTTACAGACCCT 59.422 50.000 0.00 0.00 0.00 4.34
720 1442 3.309954 CCGTACGTACTTACAGTCCCTAC 59.690 52.174 22.55 0.00 0.00 3.18
759 1481 3.788227 ATCAAACCTTGTACTGCTCCA 57.212 42.857 0.00 0.00 0.00 3.86
788 1733 2.183478 AACGTCACAAGATGCCATGA 57.817 45.000 0.00 0.00 33.96 3.07
789 1734 2.226200 TCAAACGTCACAAGATGCCATG 59.774 45.455 0.00 0.00 33.96 3.66
869 2454 4.504858 ACTGTTAAACATAGAGCGGGAAG 58.495 43.478 0.00 0.00 0.00 3.46
876 2461 8.842358 TGGGACTTAAACTGTTAAACATAGAG 57.158 34.615 0.00 0.00 0.00 2.43
884 2469 8.789762 GCTTAATTCTGGGACTTAAACTGTTAA 58.210 33.333 0.00 0.00 0.00 2.01
885 2470 8.161425 AGCTTAATTCTGGGACTTAAACTGTTA 58.839 33.333 0.00 0.00 0.00 2.41
886 2471 7.004691 AGCTTAATTCTGGGACTTAAACTGTT 58.995 34.615 0.00 0.00 0.00 3.16
887 2472 6.431234 CAGCTTAATTCTGGGACTTAAACTGT 59.569 38.462 10.12 0.00 31.95 3.55
888 2473 6.431234 ACAGCTTAATTCTGGGACTTAAACTG 59.569 38.462 13.84 13.84 37.14 3.16
889 2474 6.543735 ACAGCTTAATTCTGGGACTTAAACT 58.456 36.000 8.98 0.00 35.94 2.66
1029 2620 0.891373 CGCTATCTCGATGGTGGGAT 59.109 55.000 0.00 0.00 0.00 3.85
1055 2667 0.108615 ACAGCTACGACTGCACATCC 60.109 55.000 0.00 0.00 41.60 3.51
1186 2804 1.304381 GCATTGTGGAGGCTCCCAA 60.304 57.895 30.03 28.90 38.06 4.12
1947 3577 2.281484 GCGTTGGCCTCCTTGACA 60.281 61.111 3.32 0.00 0.00 3.58
1968 3598 2.906182 CTTCGTGCAGCCGGCTCATA 62.906 60.000 30.29 13.36 45.15 2.15
1986 3616 3.893763 CGCTCCTCGATGACGGCT 61.894 66.667 0.00 0.00 41.67 5.52
2021 3651 1.536943 AAGCTCCTTTCTCTCGCCGT 61.537 55.000 0.00 0.00 0.00 5.68
2055 3685 1.001293 TCTTTGAGCGTGATGAGCACT 59.999 47.619 0.00 0.00 45.49 4.40
2338 4015 3.000819 TTCGCCATCACCTCCGGT 61.001 61.111 0.00 0.00 35.62 5.28
2525 4207 2.441750 GACATGGCTTCCCTTGGGTATA 59.558 50.000 5.51 0.00 39.84 1.47
2572 4254 0.326618 ATCCCAGATGGTCGGGTTCT 60.327 55.000 0.00 0.00 43.57 3.01
2699 4405 2.268076 GCACATTGCCGTCCCAAGT 61.268 57.895 0.00 0.00 37.42 3.16
2875 4581 4.933330 TCCGAAGATATATTAGATGGCGC 58.067 43.478 0.00 0.00 0.00 6.53
2930 4637 1.002366 GCTCACATCATGGTGACGAC 58.998 55.000 14.29 0.00 42.56 4.34
2932 4639 1.423721 CGGCTCACATCATGGTGACG 61.424 60.000 14.29 6.82 42.56 4.35
2984 4691 1.601162 GCCAAGAACATGTGTGCACAG 60.601 52.381 22.40 11.69 45.48 3.66
3005 4712 0.250124 CAAGCCGGGTTGTAGTCACA 60.250 55.000 33.12 0.00 0.00 3.58
3044 4755 2.103263 AGGTTCTCGATTGGATGGCTAC 59.897 50.000 0.00 0.00 0.00 3.58
3110 4821 9.522804 CAGTAGATAGACAATTTCTCAACCTAC 57.477 37.037 0.00 0.00 35.55 3.18
3145 4856 6.074195 GCGGTTATCGTGCTAATGTATAAACA 60.074 38.462 0.00 0.00 41.72 2.83
3405 5124 4.592485 ACATGTCGTCTGTTTTCTCTCT 57.408 40.909 0.00 0.00 0.00 3.10
3504 5223 4.805719 CAGCAGCTTCATATCGAACACTAA 59.194 41.667 0.00 0.00 0.00 2.24
3516 5235 1.669779 GATTCTTCGCAGCAGCTTCAT 59.330 47.619 0.00 0.00 39.10 2.57
3517 5236 1.081892 GATTCTTCGCAGCAGCTTCA 58.918 50.000 0.00 0.00 39.10 3.02
3565 5285 6.150474 GTGGTACTTAGCATTTTTGCCTTCTA 59.850 38.462 0.00 0.00 35.99 2.10
3693 5415 6.827586 TTGCCTTAACACTTTATTGGTAGG 57.172 37.500 0.00 0.00 0.00 3.18
3757 5480 9.921637 GGTTTGAATTTTTGTGATGGTATAGAA 57.078 29.630 0.00 0.00 0.00 2.10
3763 5486 5.365021 TGGGTTTGAATTTTTGTGATGGT 57.635 34.783 0.00 0.00 0.00 3.55
3764 5487 6.690194 TTTGGGTTTGAATTTTTGTGATGG 57.310 33.333 0.00 0.00 0.00 3.51
3804 5532 5.123979 GGGTGACTTTGTATTGTTCATCTCC 59.876 44.000 0.00 0.00 0.00 3.71
3861 5591 5.487488 ACAACCTCATCCAAAGATACCTACA 59.513 40.000 0.00 0.00 0.00 2.74
3887 5617 4.759782 AGAACGACAAATCCTACCATCAG 58.240 43.478 0.00 0.00 0.00 2.90
3889 5619 4.935808 ACAAGAACGACAAATCCTACCATC 59.064 41.667 0.00 0.00 0.00 3.51
3925 5655 8.446273 ACAACGTCATAGATTTCTGAAGAATTG 58.554 33.333 0.00 0.00 33.54 2.32
4011 5744 6.686484 TCCTGGTGGTACTACTATCGTATA 57.314 41.667 9.41 0.00 34.23 1.47
4031 5764 1.065126 GGCTGAGTTGTTGCCTATCCT 60.065 52.381 0.00 0.00 43.05 3.24
4035 5768 1.142870 AGTTGGCTGAGTTGTTGCCTA 59.857 47.619 0.00 0.00 46.23 3.93
4041 5774 4.757149 GTGAGATTAAGTTGGCTGAGTTGT 59.243 41.667 0.00 0.00 0.00 3.32
4058 5791 5.163152 GGATAGGATTGTTTCAGGGTGAGAT 60.163 44.000 0.00 0.00 0.00 2.75
4074 5807 7.977818 TGTAGTTGCTCAAATATGGATAGGAT 58.022 34.615 0.00 0.00 0.00 3.24
4118 5851 0.810031 CATTACCCTCCGTTGCCGAG 60.810 60.000 0.00 0.00 35.63 4.63
4142 5875 3.004543 TCCAAATTGGATTGCCCCC 57.995 52.632 11.23 0.00 42.67 5.40
4170 5903 3.776417 ACCAGGCGGTTTAGAGGTATTTA 59.224 43.478 0.00 0.00 46.31 1.40
4173 5906 1.485066 CACCAGGCGGTTTAGAGGTAT 59.515 52.381 0.00 0.00 46.31 2.73
4227 5960 1.229177 ATTTGTGGTCCTTGGGCCC 60.229 57.895 17.59 17.59 0.00 5.80
4228 5961 1.543944 CCATTTGTGGTCCTTGGGCC 61.544 60.000 2.82 2.82 0.00 5.80
4233 5971 3.074390 TGTCTCATCCATTTGTGGTCCTT 59.926 43.478 0.00 0.00 0.00 3.36
4239 5977 3.057315 GGGTGTTGTCTCATCCATTTGTG 60.057 47.826 0.00 0.00 38.39 3.33
4288 6027 0.108329 ACATAGGGAACGCCGAAGTG 60.108 55.000 0.00 0.00 33.83 3.16
4296 6035 9.124807 GAATAAAAGAAAACAACATAGGGAACG 57.875 33.333 0.00 0.00 0.00 3.95
4327 6080 7.756272 TCCGGAAAGAGAAAACTAAAACAAAAC 59.244 33.333 0.00 0.00 0.00 2.43
4362 6129 7.389053 GCCTGTAAGAAGAGAAAATCAGAGAAA 59.611 37.037 0.00 0.00 34.07 2.52
4365 6132 6.405538 AGCCTGTAAGAAGAGAAAATCAGAG 58.594 40.000 0.00 0.00 34.07 3.35
4367 6134 6.622462 GCAAGCCTGTAAGAAGAGAAAATCAG 60.622 42.308 0.00 0.00 34.07 2.90
4369 6136 5.414144 AGCAAGCCTGTAAGAAGAGAAAATC 59.586 40.000 0.00 0.00 34.07 2.17
4576 6351 7.345914 TGAAATGAAACTCCTTTTCCCCTAAAA 59.654 33.333 0.00 0.00 42.80 1.52
4596 6376 9.613428 TGACTGTAACTCCCTAAATATGAAATG 57.387 33.333 0.00 0.00 0.00 2.32
4600 6380 8.603898 TCTTGACTGTAACTCCCTAAATATGA 57.396 34.615 0.00 0.00 0.00 2.15
4610 6390 3.402628 TTGCCTCTTGACTGTAACTCC 57.597 47.619 0.00 0.00 0.00 3.85
4622 6402 8.636213 CCATGTATTGAGAATATTTTGCCTCTT 58.364 33.333 0.00 0.00 0.00 2.85
4633 6413 5.966853 TGGACCACCATGTATTGAGAATA 57.033 39.130 0.00 0.00 41.77 1.75
4636 6416 3.054434 CCTTGGACCACCATGTATTGAGA 60.054 47.826 0.00 0.00 46.34 3.27
4648 6428 1.074775 TGGATGCACCTTGGACCAC 59.925 57.895 0.00 0.00 39.86 4.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.